You can check the update news for the games to see what's been done so far, here's a changelog:
This list covers the releases between March 20 and April 15 that are each part of a series of security updates.

Larger changes:

Added privilege checking to command execution. Commands originating outside of the client are now only able to execute commands that are considered to be safe. Commands such as 'connect', 'bind', 'quit' and certain cvars such as 'cl_filterstuffcmd' are now only executable by trusted sources.

Setting 'cl_filterstuffcmd' to a value greater than zero (e.g. 'cl_filterstuffcmd 1') will set a number of commands that are potentially abusable, such as 'say', 'fps_max', and 'setinfo', to also be only executable by privileged sources.

Fixes:

Fixed intermittent double weapon firing (TFC only)

Fixed client incorrectly blocking download of custom sprays

Security fixes:

All custom resources downloaded from a server now have their file name's checked for safety before being allowed to download

Invalid file extensions are now prevented in several commands

Dynamic libraries are no longer searched for in custom resource directories